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It's not clear to me when we want to merge in these changes; it might be that we want to do so ASAP so that we start getting snapshots with...

sierra-moxon

MGI GAF includes PRO isoforms as the main annotatable object

10

``` ✗ getgaf mgi | egrep '\tprotein\t' | tail PR Q9Z2D6-2 mMECP2/iso:2 located_in GO:0005634 PMID:18334558 IDA C methyl-CpG-binding protein 2 isoform 2 (mouse) mMECP2/iso:2|MECP2b (mouse)|MECP2e1 (mouse) protein taxon:10090 20120126MGI PR...

cmungall

This is not for the immediate future, but oit would be very useful to validate files against the GPIs that groups provide.

pgaudet

Create end-user GAF validation SOP / tooling

1

This is coming out of a meeting and email thread with Markus K. The given file is currently at: http://skyhook.berkeleybop.org/ecocyc-2024-04-19-upstream.gaf.gz The idea would be to either provide a "simple" SOP...

kltm

ZFIN GAF contains uncommented metadata

3

Found during a scan for https://github.com/geneontology/go-site/issues/2246, the following ZFIN metadata is in error: ``` 0.001!date-generated: 2024-03-14 ```

kltm

clarify gorule-0000023, annotation propagation, regarding propagation of redundant annotations

4

https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000023.md includes: ``` TBD Should this pipeline filter annotations based on some redundancy criteria? ``` (I think the intention is to say "Should this _rule_ filter"...) I don't think any...

cmungall

Provide GPAD/GPI 2.0 examples for public use

2

Closing this ticket means that @pgaudet has been provided a sufficiently final version of any example file(s) for GPAD / GPI 2.0, so that she can: - let downstreams know...

kltm

sierra-moxon

Make (and use) isoform promotion GORULE

4

As part of @sierra-moxon 's work, we explicitly made the choice to have the following data transform: when there is an isoform available in the GPI, use that as the...

kltm

Should contains: !gaf-version: !generated-by: database listed in dbxrefs.yaml !date-generated: YYYY-MM-DD or YYYY-MM-DDTHH:MM Example errors in https://github.com/geneontology/go-site/issues/2246 reactome-src.gaf.gz:date-generated: 2023-12-01 reactome-src.gaf.gz:generated-by: Reactome reactome-src.gaf.gz:Project-release: Version 87 zfin-src.gaf.gz:0.001!date-generated: 2024-03-14 - [ ] complete the...

pgaudet